needed recipes

[arq5x]

• Ensembl all exons from protein-coding genes and isoforms for all human builds in GTF format

• Ensembl coding exons from protein-coding genes and isoforms for all human builds in GTF format

• Ensembl introns from protein-coding genes and isoforms for all human builds in GTF format

• Microsatellites (excluding GRCh38 because of mapping file)

• Cytobands (excluding GRCh38 because of mapping file)

• chromosome sizes

• CCRs

• gnomAD SVs

• CCDG SVs

• ClinVar

• Recombination Maps

• Vista Enhancers

• Scores used in pathoscore (see the recipes there)
  - Truth Sets: https://github.com/quinlan-lab/pathoscore/tree/master/truth-sets/GRCh37
  - Gene Sets: https://github.com/quinlan-lab/pathoscore/tree/master/gene-sets/GRCh37

• Conservation tracks

• ENCODE datasets

• GTeX datasets

• HCA datasets

• pext gnomAD

• reference transcriptome

• reference proteome

• clinvar

• gencode

• cosmic

• dbsnp

  • https://ftp.ncbi.nih.gov/snp/pre_build152/organisms/human_9606_b150_GRCh37p13/VCF/GATK/

• dbscnv

• dbnsfp

• hapmap

• radar

• giab (?)

• CADD

• BRAVO/Top Med

• UCSC Tracks

• Ensembl

• dbnsfp (with postprocessing as suggested by Ensembl: https://www.ensembl.org/info/docs/tools/vep/script/vep_example.html)

• NCBI pipelines genomes, in particular the gold standard reference as suggested by Heng Li: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz

• GTF annotation track for each reference genome

• BWA, Bowtie and STAR index for each reference genome

• Reference transcriptomes for use with kallisto/salmon. Best from Ensembl

• MIG (Medically Interpretable Genes)

  • http://www.genomemedicine.com/content/pdf/s13073-015-0197-4.pdf

• ACMG regions

  • http://iobio.io/2016/03/29/acmg56/

• The Global Alliance for Genomics and Health genomic file (?)

  • https://github.com/ga4gh/benchmarking-tools/tree/master/resources/stratification-bed-files

• Mills indels

  • ftp://gsapubftp-anonymous:none@ftp.broadinstitute.org/bundle/hg19/

• small RNA seq annotation

  • http://mirbase.org/
  • https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgRna
    - https://genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=genes&hgta_track=wgRna&hgta_table=wgRna&hgta_doSchema=describe+table+schema
    - wgRna.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/wgRna.txt.gz
  • http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/tRNAs.txt.gz

• platinum genome NA12878

• RNA seq data

• Ribosom profiling data

• chip seq

• Splice AI

• Gene Splicer

• qsignature

  • https://sourceforge.net/p/adamajava/wiki/qSignature/
  • http://downloads.sourceforge.net/project/adamajava/qsignature.tar.bz2

• CCDS

  • https://www.ncbi.nlm.nih.gov/projects/CCDS/

• Exome Sequencing Project (ESP) liftover to hg38

  • http://evs.gs.washington.edu/evs_bulk_data/ESP6500SI-V2-SSA137.GRCh38-liftover.snps_indels.vcf.tar.gz

• Genotype2Phenotype (G2P) annotations

  • https://www.ebi.ac.uk/gene2phenotype/about
  • https://www.ebi.ac.uk/gene2phenotype/downloads/DDG2P.csv.gz